Showing : SingleCell • reset
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
4 months ago info ▴ 10
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370
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Job: Postdoctoral Research Associate in Computational Epigenomics
Phd SingleCell DNAMethylation Shanghai JobPosting
5 months ago xiaolong • 0
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455
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Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
9 months ago Silvio • 0
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670
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Job: Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics JobPosting SingleCell Spatial SpatialExperiment
12 months ago Peter Hickey ▴ 750
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1
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1.1k
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'Seurat' package
singlecell seurat
updated 22 months ago by ★ 4.7k • written 22 months ago by ▴ 10
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1
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1.1k
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 22 months ago by ▴ 750 • written 22 months ago by • 0
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2
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924
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
22 months ago paria.alipour • 0
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2
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1.2k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
23 months ago Assa Yeroslaviz ★ 1.5k
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4
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1.1k
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Single-cell differential expression analysis with multiple samples
SingleCell
24 months ago iaradsouza1 • 0
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8
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1.6k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 15 months ago by • 0 • written 24 months ago by • 0
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1.1k
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
24 months ago Laurent Gatto 1.6k
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3
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1.9k
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Knee and Inflection of DropletUtils
SingleCell
updated 2.0 years ago by ★ 4.7k • written 2.0 years ago by • 0
0
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1
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4.1k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 2.0 years ago by ★ 4.7k • written 2.0 years ago by • 0
1
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1
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1.1k
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 2.1 years ago by ★ 13k • written 2.1 years ago by ▴ 70
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1
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916
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.1 years ago Jenny Drnevich ★ 2.0k
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3
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1.2k
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
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1
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894
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.2 years ago by ★ 2.0k
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3
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1.8k
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 7 months ago by • 0 • written 2.3 years ago by • 0
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1
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950
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
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1.1k
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
2.4 years ago sudhir.thakurela • 0
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737
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Gene Id duplicated
SingleCell SingleCellData
updated 2.4 years ago by ★ 4.7k • written 2.4 years ago by • 0
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1
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1.0k
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 10
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706
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weighting sample group
monocle SingleCell DifferentialExpression
2.5 years ago Sogand • 0
2
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2
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1.1k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.5 years ago k1m ▴ 20
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2
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1.5k
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
2.5 years ago Guandong Shang ▴ 40
2
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4
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1.3k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.5 years ago Romina • 0
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1
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1.6k
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Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
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1
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1.7k
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Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 2.6 years ago by ★ 4.7k • written 2.6 years ago by • 0
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2
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1.9k
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
2.6 years ago fluentin44 • 0
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905
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
2.7 years ago Nik Tuzov ▴ 90
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.8 years ago zroger499 • 0
2
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1
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995
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() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 2.9 years ago by ▴ 90 • written 2.9 years ago by • 0
2
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1
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2.2k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
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1.0k
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.1 years ago zroger499 • 0
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0
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1.2k
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.1 years ago Sebastian Lewandowski • 0
2
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2
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1.5k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.2 years ago by ★ 4.7k • written 3.2 years ago by ▴ 40
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914
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
3.4 years ago lpinello • 0
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2
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1.4k
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Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
3.4 years ago Andrew Pattison • 0
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944
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Spike-In Cells for Normalization?
SpikeIn SingleCell
3.5 years ago mb1996 • 0
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952
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
3.6 years ago camp ▴ 10
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1.2k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.6 years ago lianov • 0
0
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1
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1.2k
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
3
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2
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3.0k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.1 years ago camerond • 0
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0
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1.3k
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
4.2 years ago Steve Lianoglou ★ 13k
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2
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1.8k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.2 years ago jirkanov • 0
3
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1
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2.2k
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DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 10
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1
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1.1k
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 50
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1.0k
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.3 years ago hamza_karakurt ▴ 60
2
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6
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2.8k
views
Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 50
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6
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3.3k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 80
50 results • Page 1 of 1
Recent ...
Replies
Answer: Is it possible to model DNA methylation as a dose response in edgeR? by Gordon Smyth 52k
edgeR works with any linear model, so handles any combination of factors and covariates. If you include dose as a covariate in the linear m…
Comment: DepMap data mismatch by Laurent Gatto 1.6k
It might be due to different versions. The repacked/cleaned data in the `depmap` R/Bioconductor package is old, but the latest files can al…
Comment: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k
If you are using `conumee2`, then you are in the wrong place. That isn't a Bioconductor package (yet? No idea if they have/will submit it).
Answer: myvariant error by James W. MacDonald 68k
You don't show anything about the data you are annotating, so it's hard to say what the problem might be. Does the example data work for yo…
Answer: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k
There doesn't appear to be a function called `CNV.summaryplot` in `conumee`. What package does that function come from?
Votes
A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Awards • All
Popular Question to Laurent Gatto 1.6k
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Popular Question to svlachavas ▴ 840
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
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